Macular: a multi-scale simulation platform for the retina and the primary visual system

We developed Macular, a simulation platform with a graphical interface, designed to produce in silico experiment scenarios for the retina and the primary visual system. A scenario consists of generating a three-dimensional structure with interconnected layers, each layer corresponding to a type of ‘cell’ in the retina or visual cortex. The cells can correspond to neurons or more complex structures (such as cortical columns). The inputs are arbitrary videos. The user can use the cells and synapses provided with the software, or create their own using a graphical interface where they enter the constituent equations in text format (e.g., LaTeX). They also create the three-dimensional structure via the graphical interface. Macular then automatically generates and compiles the C++ code and generates the simulation interface. This allows the user to view the input video and the three-dimensional structure in layers. It also allows the user to select cells and synapses in each layer and view the activity of their state variables. Finally, the user can adjust the phenomenological parameters of the cells or synapses via the interface. We provide several example scenarios, corresponding to published articles, including an example of a retino-cortical model. Macular was designed for neurobiologists and modelers, specialists in the primary visual system, who want to test hypotheses in silico without the need for programming. By design, this tool allows natural or altered conditions (pharmacology, pathology, development) to be simulated.

💡 Research Summary

Macular is a groundbreaking multi-scale simulation platform specifically engineered to model the intricate dynamics of the retina and the primary visual system. The primary objective of this platform is to empower neurobiologists and computational modelers to conduct sophisticated in silico experiments without the heavy burden of traditional programming. By providing a user-friendly graphical interface, Macular enables the creation of complex, three-dimensional neural architectures consisting of interconnected layers, which can represent various biological scales, from individual neurons to large-scale cortical columns.

A defining technical achievement of Macular is its seamless integration of mathematical modeling and high-performance computing. The platform allows users to define the physiological properties of cells and synapses using LaTeX-formatted equations. Once these equations are entered via the GUI, Macular’s automated engine generates, compiles, and executes the corresponding C++ code. This approach effectively bridges the gap between high-level biological abstraction and low-level computational efficiency, providing a “low-code” environment that retains the rigorous performance of C++.

The platform’s versatility is further enhanced by its ability to process arbitrary video inputs as visual stimuli. This allows researchers to subject their neural models to realistic visual sequences, observing how information is processed through the retinal layers and into the visual cortex. The integrated visualization suite allows for real-time monitoring of specific cellular state variables and the spatial arrangement of the 3D structure, alongside the input video stream, facilitating a deep comparative analysis of stimulus and response.

Beyond simple simulation, Macular is designed to act as a versatile laboratory for testing biological hypotheses under diverse conditions. Through the intuitive adjustment of phenomenological parameters, researchers can simulate natural visual processing as well as altered physiological states, including the effects of pharmacological interventions, pathological conditions such as retinal degeneration, and the complex processes of neural development. By enabling the large-scale simulation of complex neural circuits, Macular provides a powerful tool for exploring the fundamental mechanisms of the visual system and advancing our understanding of neurobiology.